Analysis module 3: Geographic differences in 16S microbiota composition RoVI study — 31 October, 2020

Sidebar

Sample summary

Taxon abundance profile

Alpha diversity

Longitudinal abundance plots

Beta diversity

Differential taxa

Longitudinal abundance comparisons

Sample summary

Input data: infant stools (BS1, BS2, BS3, and BS5) and maternal stool (MS1)

  • n samples = 2086
  • n taxa: genera = 487; variants = 6239
  • n taxa (rarefied): genera = 453; variants = 6103
  • mean read count = 1.428810^{5}, s.d. = 1.358610^{5}

Statistical methods for mixed-effects models

  • Linear mixed-effects models fit with family ID as a random effect
  • Effect of country determined by comparing: (i) model with country/age vs (ii) model with age alone
  • Pairwise comparisons between countries (M vs I, U vs I, U vs M) corrected by FDR to control family error rate
  • OPV/IPV arms from India combined in primary comparison
  • Diversity in maternal samples compared by country via ANOVA with post-hoc Tukey test

Taxon abundance profile

Column

Genus-level

India - infant

Malawi - infant

UK - infant

India - maternal

Malawi - maternal

UK - maternal

RSV-level

India - infant

Malawi - infant

UK - infant

India - maternal

Malawi - maternal

UK - maternal

Alpha diversity

Column

Genus-level

India vs Malawi vs UK

p values (FDR-adjusted, 4 decimal places)

             Shannon Richness
Malawi-India  0.0000   0.0000
UK-India      0.2133   0.4976
UK-Malawi     0.0322   0.0000

p values, India (OPV) vs India (IPV)

                        Shannon Richness
India (OPV)-India (IPV)  0.4666   0.2373

Maternal samples

p values, India vs Malawi vs UK

             Shannon Richness
Malawi-India  0.9782   0.1271
UK-India      0.0001   0.0001
UK-Malawi     0.0029   0.0000

p values, India (OPV) vs India (IPV)

  Shannon Richness
1  0.6511   0.8167

RSV-level

India vs Malawi vs UK

p values (FDR-adjusted, 4 decimal places)

             Shannon Richness
Malawi-India  0.0000   0.0000
UK-India      0.0032   0.6661
UK-Malawi     0.3792   0.0010

p values, India (OPV) vs India (IPV)

                        Shannon Richness
India (OPV)-India (IPV)  0.5419   0.7797

Maternal samples

p values, India vs Malawi vs UK

             Shannon Richness
Malawi-India   0.000    0e+00
UK-India       0.054    6e-04
UK-Malawi      0.000    0e+00

p values, India (OPV) vs India (IPV)

  Shannon Richness
1  0.6978   0.8935

Longitudinal abundance plots

Infants - India vs UK vs Malawi

Infants - India (OPV) vs India (IPV)

Maternal samples (with genera corresponding to infant plots included)

Beta diversity

Column

Genus-level

Bray-Curtis distances (weighted)

Bray-Curtis distances (unweighted)

Turnover, paired vs random (weighted)

For week 1, distance from maternal sample plotted. For subsequent samples, distance from prior infant sample plotted.

Turnover, paired vs random (unweighted)

Longitudinal samples from a given infant more closely clustered than expected by chance in each of the three cohorts.

RSV-level

Bray-Curtis distances (weighted)

Bray-Curtis distances (unweighted)

Turnover, paired vs random (weighted)

For week 1, distance from maternal sample plotted. For subsequent samples, distance from prior infant sample plotted.

Turnover, paired vs random (unweighted)

Longitudinal samples from a given infant more closely clustered than expected by chance in each of the three cohorts.

Differential taxa

Column

Genus-level

Cross-validation accuracy, India vs Malawi vs UK

Cross-validation accuracy, India (OPV) vs India (IPV)

Pre-vaccination comparisons (main manuscript figure)

Grid of all other comparisons

Differential prevalence plots

RSV-level

Cross-validation accuracy, India (OPV) vs Malawi vs UK

Cross-validation accuracy, India (OPV) vs India (IPV)

Pre-vaccination comparisons

Grid of all other comparisons

Differential prevalence plots

Longitudinal abundance comparisons

India vs UK

Number of genera tested: 31
Number of discriminant genera (FDR p < 0.1): 25 (India = 14; UK = 11) Failed to converge: 0

India vs Malawi

Number of genera tested: 42
Number of discriminant genera (FDR p < 0.1): 29 (India = 8; Malawi = 21) Failed to converge: 0

Malawi vs UK

Number of genera tested: 44
Number of discriminant genera (FDR p < 0.1): 31 (Malawi = 22; UK = 9) Failed to converge: 0

Construct tree

Longitudinal abundance plots for major genera